It took 14 years, but the owners of the now-decommissioned Yankee Atomic Electric plant in Rowe have won a $38.3 million settlement from the federal government for its failure to meet a contractual obligation to take possession of high-level radioactive waste in 1998.

In 2003, Yankee’s then-President Rick Kacich said, “The 1998 lawsuit against the DOE was filed to protect electric customers who bear the cost of storing the fuel at the plant sites until the federal government finally removes it. Because the DOE has failed to remove the fuel, it must continue to be safely stored and protected at Yankee Rowe, leaving regional electric consumers to bear the financial burden of the federal government’s inaction.”

The damages — part of a nearly $160 million settlement for the Yankee Atomic Electric Co., the Maine Yankee Atomic Power Company and the Connecticut Yankee Atomic Power Co. — are the first of several phases of the litigation.

The Rowe plant, which shut down in 1992 and was at the time the nation’s oldest commercial nuclear reactor, was decommissioned in 2007, and 533 radioactive spent-fuel assemblies remain on site in a protected dry-cask storage area.

The entire $160 million settlement, minus state and federal taxes, will eventually flow back to ratepayers, according to “existing regulatory agreements,” said a statement from the three plants’ owners on Wednesday. The damage award funds were transferred from the U.S. Treasury to the three companies and have been deposited into trust funds.

The companies, each owned by a consortium of New England utilities, plan to file in coming months with the Federal Energy Regulatory Commission their plans for “the best way to use the proceeds from the damage awards to benefit the ratepayers.” Among those owners are National Grid, with a 34.5 percent share, and Western Massachusetts Electric Co., 7 percent.

The federal government chose not to appeal a May 18, 2012, U.S. Court of Appeals judgment confirming awards of $39.7 million for Connecticut Yankee and $81.7 million for Maine Yankee, and increasing the award for Yankee Rowe to $38.3 million. In that case, the Appeals Court agreed with the company’s position that the Court of Federal Claims had erred in excluding from the Rowe settlement those costs related to storage of the waste before the assemblies could be transferred from wet to dry storage in 2002 and 2003.

Under the 1982 Nuclear Waste Policy Act, the spent fuel assemblies at the commercial plants legally became property of the federal Department of Energy in 1998, and the Court of Appeals agreed that year that the government, unable to site a waste repository at Nevada’s Yucca Mountain, was in breach of its contract to remove the high-level waste from the reactors.

A Department of Justice spokesman was not available for comment.

According to an energy department inspector general’s report issued last November, Yankee’s first-in-the-nation case was one of 74 filed for Nuclear Waste Fund damages for nuclear waste storage, of which 31 had been settled at a cost of nearly $2 billion.

Because the courts ruled that the plant owners could not seek future damages from DOE, the settlements are being sought in three phases. The three Yankee companies are now seeking approximately $247 million in additional damages for the second round of cases that were filed with Federal Claims court in 2007. This includes $76.6 million for Yankee Rowe’s owner, reflecting damages from 2002 through 2008. The trial was held in October 2011, with the most recent round of post-trial briefings concluded last Dec. 17.

Plant owners say they hope Judge James F. Merow will issue his decision in these cases “shortly,” and that they anticipate filing for a third round of damages claims by the end of this year. But a company spokesman said there is no limit to how many rounds of funding may be sought from the Federal Judgment Fund. “We will continue to seek damages to recover the annual costs of storing the material until the government meets its obligation to remove the waste from the site.”

“We are very pleased that after 14 years of litigation the three companies have recovered for our ratepayers nearly $160 million in costs resulting from the Department of Energy’s failure to remove spent nuclear fuel and Greater than Class C waste from our three sites,” said Yankee President Wayne Norton. “These funds, and additional damages claims we hope to recover in the future, will all benefit our ratepayers.”

The settlement doesn’t result in the radioactive waste being removed from the three plant sites, said Norton.

“However, we are pleased that in the DOE’s Jan. 11 strategy report the administration supports an integrated nuclear waste management system that includes a pilot interim storage facility with an initial focus on accepting spent nuclear fuel from shut-down reactor sites. We are hopeful Congress and the Administration will move immediately to implement the report recommendations and we look forward to working with others to bring that about,” said Norton.

Current annual costs to operate the spent fuel storage total $7 to $11 million, although company officials said those costs could increase as additional regulations potentially impose more requirements on the companies.